Abstract Defecation in the ctenophore Mnemiopsis leidyi is a stereotyped sequence of effector responses that occur with a regular ultradian rhythm. Here I used video microscopy to describe new features and correct previous reports of the gastrovascular system during and between defecations. Contrary to the scientific literature, individuals defecated through only one of the two anal canals which possesses the only anal pore. The anal pore was not visible as a permanent structure as depicted in textbooks, but appeared at defecation and disappeared afterward. Time intervals between repeated defecations in individual animals depended on body size, ranging from ~10 min in small larvae to ~1 hr in large adults. Differential interference contrast microscopy revealed that both the opening and closing of the anal pore resembled a reversible ring of tissue fusion between apposed endodermal and ectodermal layers at the aboral end. Individuals of M. leidyi thus appear to have an intermittent anus and therefore an intermittent through-gut that reoccur at regular intervals. The temporality of a visible anal pore in M. leidyi is novel, and may shed light on the evolution of a permanent anus and through-gut in animals. In addition, mirror image dimorphism of the diagonal anal complex occurs in larval ctenophores but not in adults, indicating developmental flexibility in diagonal symmetry of the anal complex.